Query 040493
Match_columns 69
No_of_seqs 13 out of 15
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 09:00:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00105 L31 ribosomal protei 99.6 1.2E-15 2.7E-20 93.9 3.8 58 1-60 1-67 (68)
2 PRK00528 rpmE 50S ribosomal pr 99.4 1.4E-13 3E-18 85.6 4.3 60 1-60 1-70 (71)
3 PF01197 Ribosomal_L31: Riboso 99.4 2.1E-14 4.5E-19 88.4 -3.3 60 1-60 1-68 (69)
4 PRK01678 rpmE2 50S ribosomal p 99.2 7.3E-12 1.6E-16 81.4 3.5 63 1-63 1-83 (87)
5 PRK01397 50S ribosomal protein 99.2 1.1E-11 2.4E-16 79.1 3.8 59 1-62 1-70 (78)
6 PRK00019 rpmE 50S ribosomal pr 99.2 1.2E-11 2.6E-16 77.7 3.8 59 1-61 1-68 (72)
7 CHL00136 rpl31 ribosomal prote 99.2 1.1E-11 2.5E-16 77.1 3.5 55 1-59 2-66 (68)
8 COG0254 RpmE Ribosomal protein 98.8 4.2E-09 9.1E-14 67.3 3.4 63 1-63 1-72 (75)
9 cd01273 CED-6 CED-6 Phosphotyr 85.5 3.6 7.7E-05 27.4 5.5 50 9-60 82-139 (142)
10 cd01274 AIDA-1b AIDA-1b Phosph 84.2 4.5 9.8E-05 26.9 5.5 52 6-60 66-125 (127)
11 cd01214 CG8312 CG8312 Phosphot 81.1 2.6 5.7E-05 29.3 3.6 42 8-49 66-115 (133)
12 cd01267 CED6_AIDA1b Phosphotyr 80.4 8.9 0.00019 24.7 5.7 50 9-60 72-130 (132)
13 PF14283 DUF4366: Domain of un 62.6 13 0.00029 27.2 3.8 31 9-39 73-103 (218)
14 PF09776 Mitoc_L55: Mitochondr 62.0 6.1 0.00013 27.2 1.8 22 4-25 39-60 (116)
15 PF00129 MHC_I: Class I Histoc 53.5 31 0.00067 22.7 4.1 38 4-41 1-39 (179)
16 cd01208 X11 X11 Phosphotyrosin 51.4 39 0.00085 24.2 4.5 49 9-60 77-149 (156)
17 cd01268 Numb Numb Phosphotyros 47.7 59 0.0013 22.3 4.8 44 8-51 76-127 (138)
18 COG4148 ModC ABC-type molybdat 40.6 18 0.0004 29.2 1.7 26 6-31 72-97 (352)
19 PF08460 SH3_5: Bacterial SH3 39.3 34 0.00073 20.5 2.3 13 10-22 49-61 (65)
20 cd01270 DYC-1 DYC-1 (DYB-1 bin 39.0 25 0.00055 24.5 2.0 25 6-31 80-104 (140)
21 smart00462 PTB Phosphotyrosine 36.0 1E+02 0.0022 18.8 5.5 53 9-63 71-130 (134)
22 PHA02754 hypothetical protein; 35.6 58 0.0013 20.9 3.1 19 9-27 34-52 (67)
23 smart00674 CENPB Putative DNA- 33.4 24 0.00051 19.7 1.0 17 45-61 47-63 (66)
24 cd07429 Cby_like Chibby, a nuc 30.9 49 0.0011 22.4 2.3 38 29-67 45-89 (108)
25 PF13953 PapC_C: PapC C-termin 30.9 27 0.00059 20.3 1.0 24 10-36 23-46 (68)
26 PF00640 PID: Phosphotyrosine 30.5 1.3E+02 0.0029 18.3 5.4 51 9-61 79-137 (140)
27 PF11102 Cap_synth_GfcB: Group 26.2 74 0.0016 22.0 2.6 20 4-23 61-85 (200)
28 PF02762 Cbl_N3: CBL proto-onc 24.5 58 0.0013 21.8 1.7 15 8-22 37-52 (86)
29 cd03285 ABC_MSH2_euk MutS2 hom 24.4 1.8E+02 0.0038 20.3 4.2 43 2-51 3-53 (222)
30 PF03221 HTH_Tnp_Tc5: Tc5 tran 23.7 45 0.00098 18.1 1.0 18 43-60 45-62 (66)
31 PHA02616 VP2/VP3; Provisional 22.9 42 0.00091 26.1 0.9 23 2-24 160-182 (259)
32 TIGR03667 Rv3369 PPOX class pr 22.1 2.2E+02 0.0048 18.1 5.1 35 8-42 15-49 (130)
33 PF11673 DUF3269: Protein of u 22.0 68 0.0015 20.8 1.6 19 49-67 47-65 (73)
34 COG2130 Putative NADP-dependen 21.3 48 0.001 26.7 1.0 16 40-55 159-174 (340)
35 PF10365 DUF2436: Domain of un 20.2 1E+02 0.0023 22.6 2.5 37 7-43 116-153 (161)
36 KOG4521 Nuclear pore complex, 20.2 73 0.0016 30.1 2.0 44 4-47 202-261 (1480)
No 1
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=99.58 E-value=1.2e-15 Score=93.95 Aligned_cols=58 Identities=21% Similarity=0.427 Sum_probs=52.0
Q ss_pred CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493 1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~ 60 (69)
|||||||..+.|.++.++|..+.+.+|+... .+. .|+|++++..+.|+|+||++||+.
T Consensus 1 MKk~IHP~y~~v~~~~s~g~~f~~~ST~~~~--~i~vdi~s~~HPfyTG~~~~~~~~GRv~KF~kry~~ 67 (68)
T TIGR00105 1 MKKDIHPDYHEITVTCTCGNVFTTRSTWGKE--TLNLDICSKCHPFYTGKQKIVDTGGRVDKFNKKFGG 67 (68)
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEeeecCCc--eEEEEECCCCcccCCCceEEeccCCcHHHHHHHhcC
Confidence 9999999999999999999999999998543 133 799999999999999999999973
No 2
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=99.43 E-value=1.4e-13 Score=85.56 Aligned_cols=60 Identities=23% Similarity=0.343 Sum_probs=52.1
Q ss_pred CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEe-hhhhhhHhhhhHHHHHHHhhh
Q 040493 1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFR-ARRQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~-aKrqma~s~GQiAKFKRRf~~ 60 (69)
|||||||..+-+.++.++|..+-+.+|.-.....+. .|+ |+..+..+.|+|+||++||+.
T Consensus 1 MKk~IHP~y~~v~~~~~~g~~f~~~ST~g~~~~~i~vdv~s~~HPfyT~G~q~~~d~~GRv~kF~kky~~ 70 (71)
T PRK00528 1 MKKDIHPDYHPIKVVMTDGTEYETRSTWGKTGPELRLDIDSGNHPAWTGGTQKLLDTGGRVAKFNKKFGG 70 (71)
T ss_pred CCCCCCCCCEEEEEEEeCCCEEEEEEcCCCCCCeEEEEECCCCCccEeCCcCeEecccCcHHHHHHHHcc
Confidence 999999999999999999999999998733333333 799 999999999999999999974
No 3
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=99.35 E-value=2.1e-14 Score=88.40 Aligned_cols=60 Identities=27% Similarity=0.495 Sum_probs=48.8
Q ss_pred CCCCccccceEEEEEee-cCeEEeeEEeEEeecceEE-------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493 1 MKKGLHPQMQWISYVTQ-SGRLMHVMMTKIHNVGKVY-------HFRARRQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq-~Grl~~vmmt~~~~~gkvy-------h~~aKrqma~s~GQiAKFKRRf~~ 60 (69)
|||||||++++|.++.. .|..+.+.+|+....=+|= .|+|++.+.++.|+|+||++||+.
T Consensus 1 MKk~IHP~y~~v~v~c~s~g~~~~~~St~~~~~~~vdi~s~~HPfytG~~~~~~~~Grv~KF~kkf~~ 68 (69)
T PF01197_consen 1 MKKGIHPEYREVKVTCSSCGNTFETRSTKEYPVIKVDICSNCHPFYTGKQKVVDTAGRVEKFNKKFGK 68 (69)
T ss_dssp --SSTSSSHCEEEEEES-SSSCECECSSSSES-EEECSCSSSSCTTCSCSSCSCCCCCCTSCCTCCCC
T ss_pred CCCCCCCCCEEEEEEEcCCCCEEEEEECCcceEEEEeecCCCCEEEcCcEEEEccccCHHHHHHHHcC
Confidence 89999999999999988 8999999999832211111 799999999999999999999974
No 4
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=99.23 E-value=7.3e-12 Score=81.36 Aligned_cols=63 Identities=27% Similarity=0.496 Sum_probs=54.4
Q ss_pred CCCCccccceEEEEE-eecCeEEeeEEeEEeec------ceE---E----------EEehhhhhhHhhhhHHHHHHHhhh
Q 040493 1 MKKGLHPQMQWISYV-TQSGRLMHVMMTKIHNV------GKV---Y----------HFRARRQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 1 mkKGlHPqmq~Is~V-tq~Grl~~vmmt~~~~~------gkv---y----------h~~aKrqma~s~GQiAKFKRRf~~ 60 (69)
|||||||..+-|.++ .+.|..+.+.+|+.... |+- + -|+|+.....+.|+|+||++||+.
T Consensus 1 MKk~IHP~y~~v~~~~~t~g~~f~~~ST~~~~~t~~~~dg~~yp~i~vdi~S~~HPFyTGkq~~vdt~GRVekF~kry~~ 80 (87)
T PRK01678 1 MKKGIHPEYRPVVFHDTSTGFKFLTGSTITTDETIEWEDGKTYPLVKVEISSASHPFYTGKQKFVDTEGRVEKFNKRFGR 80 (87)
T ss_pred CCCCCCCCCEEEEEEECCCCCEEEEeeeccccceeeecCCcccceEEEEeCCCCCCcCcCCeeEeccCCcHHHHHHHHhh
Confidence 999999999999999 68999999999986432 442 2 799999999999999999999997
Q ss_pred hhh
Q 040493 61 QAD 63 (69)
Q Consensus 61 ~~~ 63 (69)
...
T Consensus 81 ~~~ 83 (87)
T PRK01678 81 FAS 83 (87)
T ss_pred hhh
Confidence 754
No 5
>PRK01397 50S ribosomal protein L31; Provisional
Probab=99.22 E-value=1.1e-11 Score=79.07 Aligned_cols=59 Identities=22% Similarity=0.409 Sum_probs=49.0
Q ss_pred CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhh-h-hHhhhhHHHHHHHhhhhh
Q 040493 1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQ-M-AQSIGQVAKFRRRYEQQA 62 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrq-m-a~s~GQiAKFKRRf~~~~ 62 (69)
|||||||..+-|.+.. +|..+.+.+|+.. ..+. -|+|+.+ + ..+.|+|+||++||+.+.
T Consensus 1 MKk~IHP~y~~v~~~~-~G~~f~~~ST~~~--~~i~vdi~s~~HPFyTG~q~~~vdt~~GRVeKF~kry~~~~ 70 (78)
T PRK01397 1 MKSGIHPEYKKFLIKV-GSDVFETMSTHPT--GEILMDVDFRKHPAWNKDSGNVVNQSNKSVSDFNKRFSGLS 70 (78)
T ss_pred CCCCCCCCCEEEEEEE-CCCEEEEeECCCC--CcEEEEeCCCCCCcCcCCeeEEecCCCccHHHHHHHHcCcc
Confidence 9999999999999886 8999999999842 2233 7999965 3 456899999999999884
No 6
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=99.22 E-value=1.2e-11 Score=77.73 Aligned_cols=59 Identities=19% Similarity=0.487 Sum_probs=51.7
Q ss_pred CCCCccccceEEEEEeecCeEEeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhhhh
Q 040493 1 MKKGLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYEQQ 61 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~~~ 61 (69)
|||||||..+-|.++-..|..|.+.+|.... .+. -|+|++.+..+.|+|+||++||+..
T Consensus 1 MKk~IHP~y~~v~~~c~~g~~f~~~ST~~~~--~i~vdi~s~~HPFyTG~q~~~dt~GRvekF~kry~~~ 68 (72)
T PRK00019 1 MKKDIHPKYEEVTVTCSCGNVFETRSTLGKD--EINVDVCSKCHPFYTGKQKIVDTGGRVERFNKRFGKK 68 (72)
T ss_pred CCCCCCCCCEEEEEEECCCCEEEEeecCCCC--cEEEEeCCCCCCcCcCCEeEeccCCcHHHHHHHhccc
Confidence 9999999999999999999999999995322 233 7999999999999999999999865
No 7
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=99.21 E-value=1.1e-11 Score=77.13 Aligned_cols=55 Identities=29% Similarity=0.443 Sum_probs=45.3
Q ss_pred CCCCccccceEEEEEeecCeE-EeeEEeEEeecceEE---------EEehhhhhhHhhhhHHHHHHHhh
Q 040493 1 MKKGLHPQMQWISYVTQSGRL-MHVMMTKIHNVGKVY---------HFRARRQMAQSIGQVAKFRRRYE 59 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~Grl-~~vmmt~~~~~gkvy---------h~~aKrqma~s~GQiAKFKRRf~ 59 (69)
|||||||..+.+..|+-+|.. +.+-+|+ +.+. .|+|++.+..+.|+|+||++||+
T Consensus 2 MKk~IHP~y~~~~~v~c~~~~~~~~~ST~----~~i~vdv~s~~HPfyTG~~~~~~~~Grv~kF~kr~~ 66 (68)
T CHL00136 2 PKKNIHPQWFPETKVYCDGQLVMTVGSTK----PELNVDIWSGNHPFYTGSQKIIDTEGRVERFMKKYG 66 (68)
T ss_pred CCCCCCCCceeeEEEEEcCCCEEEEeecC----CCEEEEeCCCCCccCcCCeeEecccccHHHHHHHhC
Confidence 899999999877666666666 7776665 3343 79999999999999999999997
No 8
>COG0254 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]
Probab=98.81 E-value=4.2e-09 Score=67.33 Aligned_cols=63 Identities=22% Similarity=0.332 Sum_probs=49.6
Q ss_pred CCCCccccceEEEEEeec--CeEEeeEEeEEeecceEE-------EEehhhhhhHhhhhHHHHHHHhhhhhh
Q 040493 1 MKKGLHPQMQWISYVTQS--GRLMHVMMTKIHNVGKVY-------HFRARRQMAQSIGQVAKFRRRYEQQAD 63 (69)
Q Consensus 1 mkKGlHPqmq~Is~Vtq~--Grl~~vmmt~~~~~gkvy-------h~~aKrqma~s~GQiAKFKRRf~~~~~ 63 (69)
|||||||-.+..-++..+ |-.|-+.+|+....=.|= -|+|+.....+-|.|+||++||+....
T Consensus 1 MKk~IHP~y~~~v~~~~~s~g~~f~~~ST~~~~~i~vdV~s~~HPFyTG~qk~~d~~Grv~kF~kRf~~~~~ 72 (75)
T COG0254 1 MKKDIHPEYYRPVVFVCSSCGNEFTTRSTKGTDEINLDVCSKCHPFYTGKQKIVDTEGRVEKFNKRFGGFKG 72 (75)
T ss_pred CCCCcCCCccceEEEEeCCCCCEEEEEeccCCceEEEEeCCCCCCcCcCceeEeeccccHHHHHHHhccccc
Confidence 999999998665555554 999999999965521111 699999988888999999999987643
No 9
>cd01273 CED-6 CED-6 Phosphotyrosine-binding (PTB) domain. CED-6 Phosphotyrosine-binding (PTB) domain. CED6 is an adaptor protein involved in the engulfment of apoptotic cells. It has a C-terminal PTB domain, which can bind to NPXY motifs. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=85.49 E-value=3.6 Score=27.37 Aligned_cols=50 Identities=20% Similarity=0.323 Sum_probs=33.3
Q ss_pred ceEEEEEeecCeEEeeEEeEEeec---ceEE--EEehhh---hhhHhhhhHHHHHHHhhh
Q 040493 9 MQWISYVTQSGRLMHVMMTKIHNV---GKVY--HFRARR---QMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt~~~~~---gkvy--h~~aKr---qma~s~GQiAKFKRRf~~ 60 (69)
+++|||++.+...-+++.=.-.+. ++.+ .|..+. .++.++||. |...|+.
T Consensus 82 i~~ISfca~d~~~~r~FayIak~~~~~~~~~ChvF~s~~~A~~I~~tigqA--F~~ay~~ 139 (142)
T cd01273 82 LGRISFCADDKDDKRMFSFIAKAEGASGKHSCFVFTSEKLAEDITLTIGQA--FDLAYRK 139 (142)
T ss_pred cceEEEEecCCCCCeEEEEEecCCCCCCcEEEEEEeccchHHHHHHHHHHH--HHHHHHH
Confidence 789999999988777666554443 3333 444433 466788986 7777764
No 10
>cd01274 AIDA-1b AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b is an amyloid-beta precursor protein interacting protein. It consists of ankyrin repeats, a SAM domain and a C-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=84.16 E-value=4.5 Score=26.92 Aligned_cols=52 Identities=19% Similarity=0.317 Sum_probs=32.9
Q ss_pred cccceEEEEEeecCeEEeeEEeEEeecc-eEE--EEeh-h----hhhhHhhhhHHHHHHHhhh
Q 040493 6 HPQMQWISYVTQSGRLMHVMMTKIHNVG-KVY--HFRA-R----RQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 6 HPqmq~Is~Vtq~Grl~~vmmt~~~~~g-kvy--h~~a-K----rqma~s~GQiAKFKRRf~~ 60 (69)
|| |++|||++++..--+++.-.-.+.+ ..+ -|.. + ..+..++||+ |+.+|+.
T Consensus 66 ~~-i~~ISf~~~D~~d~~~FayIakd~~~~~~CHvF~~~~~~~A~~I~~tigqA--F~~ay~~ 125 (127)
T cd01274 66 HG-IYNIRCVCQDREDLNFFAYITKDTENRHYCHVFCVLTSGLAAEIITTLGQA--FEVAYQL 125 (127)
T ss_pred ee-eeEEEEEecCCCCceEEEEEeeCCCCCEEEEEEEcCCHHHHHHHHHHHHHH--HHHHHhh
Confidence 44 6999999988876555544433333 333 4442 2 4566788986 7777764
No 11
>cd01214 CG8312 CG8312 Phosphotyrosine-binding (PTB) domain. CG8312 Phosphotyrosine-binding (PTB) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=81.12 E-value=2.6 Score=29.28 Aligned_cols=42 Identities=21% Similarity=0.228 Sum_probs=32.8
Q ss_pred cceEEEEEeecCeEEeeEEeEEeecceE-----E---EEehhhhhhHhhh
Q 040493 8 QMQWISYVTQSGRLMHVMMTKIHNVGKV-----Y---HFRARRQMAQSIG 49 (69)
Q Consensus 8 qmq~Is~Vtq~Grl~~vmmt~~~~~gkv-----y---h~~aKrqma~s~G 49 (69)
.++||||.+.+-+.=+|+.-+-.+.++- . -+-.|+++|+++-
T Consensus 66 ~i~RIsYCsad~~~p~VFa~I~r~~~~~~~~~l~CHAvlC~k~~~A~aia 115 (133)
T cd01214 66 WAHRITYCVAPARYPKVFCWIYRHEGKHLKVELRCHAVLCSKPEKAQAIA 115 (133)
T ss_pred EEeeeeeecCCcCCCcEEEEEEeecccccCcceEEEEEEeCCHHHHHHHH
Confidence 4699999999999888888777777652 2 4678888888754
No 12
>cd01267 CED6_AIDA1b Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=80.39 E-value=8.9 Score=24.72 Aligned_cols=50 Identities=22% Similarity=0.311 Sum_probs=29.7
Q ss_pred ceEEEEEeecCeEEeeEEeEEeec--ceEE--EEehh-----hhhhHhhhhHHHHHHHhhh
Q 040493 9 MQWISYVTQSGRLMHVMMTKIHNV--GKVY--HFRAR-----RQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt~~~~~--gkvy--h~~aK-----rqma~s~GQiAKFKRRf~~ 60 (69)
+++|||++.+..--+++.=+-... ++.+ -|... ..+..++||. |+.+|..
T Consensus 72 i~~ISfc~~d~~~~~~FafIa~~~~~~~~~ChvF~~~~~~~A~~I~~tig~A--F~~ay~~ 130 (132)
T cd01267 72 LYNISCCAQDKEDLRFFAFIAKDTETNKHYCHVFCSEKLGLAEEIILTIGQA--FELAYRL 130 (132)
T ss_pred cceEEEEecCCCCCeEEEEEEecCCCCceEEEEEECCCHHHHHHHHHHHHHH--HHHHHHh
Confidence 689999998765444443332322 2433 34433 3567788886 7777753
No 13
>PF14283 DUF4366: Domain of unknown function (DUF4366)
Probab=62.65 E-value=13 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=26.6
Q ss_pred ceEEEEEeecCeEEeeEEeEEeecceEEEEe
Q 040493 9 MQWISYVTQSGRLMHVMMTKIHNVGKVYHFR 39 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt~~~~~gkvyh~~ 39 (69)
.|-|+++|-||.+|++..-+-..+-.||.+.
T Consensus 73 kQFiTv~Tk~gn~FyliIDr~~~~enV~fLn 103 (218)
T PF14283_consen 73 KQFITVTTKSGNTFYLIIDRDEEGENVYFLN 103 (218)
T ss_pred cEEEEEEecCCCEEEEEEecCCCcceEEEec
Confidence 4899999999999999988888877888554
No 14
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=62.02 E-value=6.1 Score=27.18 Aligned_cols=22 Identities=9% Similarity=0.126 Sum_probs=19.3
Q ss_pred CccccceEEEEEeecCeEEeeE
Q 040493 4 GLHPQMQWISYVTQSGRLMHVM 25 (69)
Q Consensus 4 GlHPqmq~Is~Vtq~Grl~~vm 25 (69)
-.+|.||-..+|-+||+|++|-
T Consensus 39 ~~Y~R~Ypv~lV~pDGSTI~Ir 60 (116)
T PF09776_consen 39 QAYARLYPVLLVRPDGSTINIR 60 (116)
T ss_pred hhhhhhccEEEEecCCCEEEEe
Confidence 3578899999999999999984
No 15
>PF00129 MHC_I: Class I Histocompatibility antigen, domains alpha 1 and 2; InterPro: IPR001039 Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response. Class I MHC glycoproteins are expressed on the surface of all somatic nucleated cells, with the exception of neurons. MHC class I receptors present peptide antigens that are synthesised in the cytoplasm, which includes self-peptides (presented for self-tolerance) as well as foreign peptides (such as viral proteins). These antigens are generated from degraded protein fragments that are transported to the endoplasmic reticulum by TAP proteins (transporter of antigenic peptides), where they can bind MHC I molecules, before being transported to the cell surface via the Golgi apparatus [, ]. MHC class I receptors display antigens for recognition by cytotoxic T cells, which have the ability to destroy viral-infected or malignant (surfeit of self-peptides) cells. MHC class I molecules are comprised of two chains: a MHC alpha chain (heavy chain), and a beta2-microglobulin chain (light chain), where only the alpha chain spans the membrane. The alpha chain has three extracellular domains (alpha 1-3, with alpha1 being at the N terminus), a transmembrane region and a C-terminal cytoplasmic tail. The soluble extracellular beta-2 microglobulin chain associates primarily with the alpha-3 domain and is necessary for MHC stability. The alpha1 and alpha2 domains of the alpha chain are referred to as the recognition region, because the peptide antigen binds in a deep groove between these two domains. This entry represents the alpha chain domains alpha1 and alpha2 that make up this recognition region (the alpha3 domain is represented by (IPR003597 from INTERPRO). More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane, 0042612 MHC class I protein complex; PDB: 1ZAG_C 1T7W_A 3ES6_A 1T7V_A 1T7Y_A 1T80_A 1T7X_A 1T7Z_A 1ZS8_C 1YPZ_A ....
Probab=53.53 E-value=31 Score=22.71 Aligned_cols=38 Identities=13% Similarity=0.162 Sum_probs=32.3
Q ss_pred CccccceEEEEEeecCeEEeeEEeEEeecceEE-EEehh
Q 040493 4 GLHPQMQWISYVTQSGRLMHVMMTKIHNVGKVY-HFRAR 41 (69)
Q Consensus 4 GlHPqmq~Is~Vtq~Grl~~vmmt~~~~~gkvy-h~~aK 41 (69)
|-|-|-+-.++|++.|...|.++.+...-|..| +|.-.
T Consensus 1 GsHsL~y~~T~~s~~~~~~p~f~~vg~vDd~~~~~Yds~ 39 (179)
T PF00129_consen 1 GSHSLRYFFTAVSQPGPGLPEFSAVGYVDDQQFLRYDSN 39 (179)
T ss_dssp -EEEEEEEEEEEEETTSSSEEEEEEEEETTEEEEEEETT
T ss_pred CCceEEEEEEEEcCCCCCCCeEeeeEEECCEEEEecCCC
Confidence 779999999999999999999999999999888 45433
No 16
>cd01208 X11 X11 Phosphotyrosine-binding (PTB) domain. X11 Phosphotyrosine-binding (PTB) domain. The neuronal protein X11 has a PTB domain followed by two PDZ domains. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether. X11 binds to the cytoplasmic domain of the beta-amyloid precursor protein (beta-APP) and does not require the substrate to be tyrosine-phosphorylated for binding.
Probab=51.39 E-value=39 Score=24.19 Aligned_cols=49 Identities=33% Similarity=0.570 Sum_probs=30.6
Q ss_pred ceEEEEEeecCeEEeeEEeEEe------------------------ecceEEEEehhhhhhHhhhhHHHHHHHhhh
Q 040493 9 MQWISYVTQSGRLMHVMMTKIH------------------------NVGKVYHFRARRQMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt~~~------------------------~~gkvyh~~aKrqma~s~GQiAKFKRRf~~ 60 (69)
|+.|||.+..|.+ -++|++-. |.=.||.=..--..++++||. |.=+|.+
T Consensus 77 L~~ISy~AD~~d~-~v~mAkr~~~~~~~~~~~~~~~~~~~~~~~~k~~ChVFes~~Aq~Ia~TIGQA--F~lAY~~ 149 (156)
T cd01208 77 LRTISYIADIGDL-VVLMARRRIPRSSSQENSEASHPSQDGKRTPKXICHVFESDEAQFIAQSIGQA--FQVAYQE 149 (156)
T ss_pred ccceEEEecCCCe-EEEEEeccccccccccccccCCcccccccccceeEEEEecCcHHHHHHHHHHH--HHHHHHH
Confidence 7999999988876 45555411 222344333345678899997 5445543
No 17
>cd01268 Numb Numb Phosphotyrosine-binding (PTB) domain. Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein, which is a determinant of asymmetric cell division. Numb has an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=47.67 E-value=59 Score=22.35 Aligned_cols=44 Identities=9% Similarity=0.196 Sum_probs=28.5
Q ss_pred cceEEEEEeecCeEEeeEEeEEeecc--e--EEEEeh-h---hhhhHhhhhH
Q 040493 8 QMQWISYVTQSGRLMHVMMTKIHNVG--K--VYHFRA-R---RQMAQSIGQV 51 (69)
Q Consensus 8 qmq~Is~Vtq~Grl~~vmmt~~~~~g--k--vyh~~a-K---rqma~s~GQi 51 (69)
.|++|||++.+...-.++.=.-.... . -+-|.+ | ..++.++||+
T Consensus 76 ~i~~ISfca~D~~d~r~FayIakd~~~~r~~CHvF~~~k~sa~~i~~avG~A 127 (138)
T cd01268 76 TIEKVSFCAPDRNFDRGFSYICRDGTTRRWMCHGFLAVKDTGERLSHAVGCA 127 (138)
T ss_pred eEEEEEEEecCCCCCcEEEEEecCCCcccEEEEEEEeeccchhHHHHHHHHH
Confidence 37899999998877776654444332 1 224444 2 3688999986
No 18
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=40.59 E-value=18 Score=29.17 Aligned_cols=26 Identities=27% Similarity=0.342 Sum_probs=21.8
Q ss_pred cccceEEEEEeecCeEEeeEEeEEee
Q 040493 6 HPQMQWISYVTQSGRLMHVMMTKIHN 31 (69)
Q Consensus 6 HPqmq~Is~Vtq~Grl~~vmmt~~~~ 31 (69)
-|.--+|+||.|+-||||-|+-+-+.
T Consensus 72 p~~~RriGYVFQDARLFpH~tVrgNL 97 (352)
T COG4148 72 PPEKRRIGYVFQDARLFPHYTVRGNL 97 (352)
T ss_pred ChhhheeeeEeeccccccceEEecch
Confidence 47778999999999999998776554
No 19
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; GO: 0016787 hydrolase activity; PDB: 1R77_B.
Probab=39.31 E-value=34 Score=20.52 Aligned_cols=13 Identities=46% Similarity=0.922 Sum_probs=8.3
Q ss_pred eEEEEEeecCeEE
Q 040493 10 QWISYVTQSGRLM 22 (69)
Q Consensus 10 q~Is~Vtq~Grl~ 22 (69)
.||||+.-||...
T Consensus 49 ~Wisy~~~sG~r~ 61 (65)
T PF08460_consen 49 VWISYISYSGQRR 61 (65)
T ss_dssp EEEEEE-TT--EE
T ss_pred EEEEEECCCCeEE
Confidence 6999999999543
No 20
>cd01270 DYC-1 DYC-1 (DYB-1 binding and Capon related) Phosphotyrosine-binding (PTB) domain. DYC-1 (DYB-1 binding and Capon related) Phosphotyrosine-binding (PTB) domain. DYC-1 contains an N-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. The PTB domains of both SHC and IRS-1, for example, bind to a NPXpY sequence. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated; whereas, other PTB domains can bind motifs lacking tyrosine residues altogether.
Probab=38.96 E-value=25 Score=24.48 Aligned_cols=25 Identities=20% Similarity=0.414 Sum_probs=18.2
Q ss_pred cccceEEEEEeecCeEEeeEEeEEee
Q 040493 6 HPQMQWISYVTQSGRLMHVMMTKIHN 31 (69)
Q Consensus 6 HPqmq~Is~Vtq~Grl~~vmmt~~~~ 31 (69)
|| +++|||++++-..-.+++-.-..
T Consensus 80 ~~-i~rISf~a~D~~~~k~FayIakd 104 (140)
T cd01270 80 HP-IYRIFYVSHDSQDLKIFSYIARD 104 (140)
T ss_pred cC-eeEEEEeecCCCCCcEEEEEecC
Confidence 45 59999999988877777654433
No 21
>smart00462 PTB Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain. PTB/PI domain structure similar to those of pleckstrin homology (PH) and IRS-1-like PTB domains.
Probab=36.04 E-value=1e+02 Score=18.78 Aligned_cols=53 Identities=26% Similarity=0.379 Sum_probs=29.9
Q ss_pred ceEEEEEeecCeEEeeEEeEEeecce--E--EEEe---hhhhhhHhhhhHHHHHHHhhhhhh
Q 040493 9 MQWISYVTQSGRLMHVMMTKIHNVGK--V--YHFR---ARRQMAQSIGQVAKFRRRYEQQAD 63 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt~~~~~gk--v--yh~~---aKrqma~s~GQiAKFKRRf~~~~~ 63 (69)
++.|||++.+-.--+++.-+..+.+. . +.|. .-..++.++||+ |+..|+....
T Consensus 71 l~~Isf~~~~~~~~~~F~fI~~~~~~~~~~CHvF~c~~~a~~i~~~i~~a--F~~a~~~~~~ 130 (134)
T smart00462 71 LRRISFCAVGPDDLDVFGYIARDPGSSRFACHVFRCEKAAEDIALAIGQA--FQLAYELKLK 130 (134)
T ss_pred ccceEEEecCCCCCcEEEEEeeCCCCCeEEEEEEEcCchHHHHHHHHHHH--HHHHHHHHHh
Confidence 48899999885444444333333332 1 1332 225677888876 6677765543
No 22
>PHA02754 hypothetical protein; Provisional
Probab=35.58 E-value=58 Score=20.89 Aligned_cols=19 Identities=26% Similarity=0.389 Sum_probs=15.4
Q ss_pred ceEEEEEeecCeEEeeEEe
Q 040493 9 MQWISYVTQSGRLMHVMMT 27 (69)
Q Consensus 9 mq~Is~Vtq~Grl~~vmmt 27 (69)
.+||+.|++||.-+-|..+
T Consensus 34 i~RIkai~~SGdkIVVi~a 52 (67)
T PHA02754 34 IDRIKAITTSGDKIVVITA 52 (67)
T ss_pred EEEEEEEEecCCEEEEEEc
Confidence 5799999999997766544
No 23
>smart00674 CENPB Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.
Probab=33.39 E-value=24 Score=19.71 Aligned_cols=17 Identities=24% Similarity=0.397 Sum_probs=14.2
Q ss_pred hHhhhhHHHHHHHhhhh
Q 040493 45 AQSIGQVAKFRRRYEQQ 61 (69)
Q Consensus 45 a~s~GQiAKFKRRf~~~ 61 (69)
..|.|=+.+||+||...
T Consensus 47 ~~s~~Wl~rF~~Rh~~~ 63 (66)
T smart00674 47 KASNGWLTRFKKRHNIV 63 (66)
T ss_pred CCCHHHHHHHHHHcCCc
Confidence 47889999999999754
No 24
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=30.95 E-value=49 Score=22.37 Aligned_cols=38 Identities=24% Similarity=0.382 Sum_probs=24.3
Q ss_pred EeecceEEEEehhhhhhH-------hhhhHHHHHHHhhhhhhhhhc
Q 040493 29 IHNVGKVYHFRARRQMAQ-------SIGQVAKFRRRYEQQADAENN 67 (69)
Q Consensus 29 ~~~~gkvyh~~aKrqma~-------s~GQiAKFKRRf~~~~~ae~~ 67 (69)
...+|+-+-|..-+=+.+ +..-+++.|||..++.| |||
T Consensus 45 l~Lg~~~l~F~dG~W~~e~~~~~~~~~~e~~rlkkk~~~LeE-ENN 89 (108)
T cd07429 45 LKLGGQELVFEDGRWISESGGSSGVSGREVLRLKKKNQQLEE-ENN 89 (108)
T ss_pred eeeCCceEEeeCCEEecCCCCCCCCchhHHHHHHHHHHHHHH-HHH
Confidence 344555554444433333 34468899999999999 775
No 25
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=30.91 E-value=27 Score=20.33 Aligned_cols=24 Identities=21% Similarity=0.347 Sum_probs=13.7
Q ss_pred eEEEEEeecCeEEeeEEeEEeecceEE
Q 040493 10 QWISYVTQSGRLMHVMMTKIHNVGKVY 36 (69)
Q Consensus 10 q~Is~Vtq~Grl~~vmmt~~~~~gkvy 36 (69)
+-|++|+++|+++ .+-+...+.|.
T Consensus 23 ~~~g~Vg~~G~vy---l~~~~~~~~L~ 46 (68)
T PF13953_consen 23 NNIGIVGQDGQVY---LSGLPPKGTLT 46 (68)
T ss_dssp SEEEEB-GCGEEE---EEEE-TCEEEE
T ss_pred CEEEEEcCCCEEE---EECCCCCcEEE
Confidence 3589999999865 33333444444
No 26
>PF00640 PID: Phosphotyrosine interaction domain (PTB/PID) A page on PI domains.; InterPro: IPR006020 The PI domain has a similar structure to the insulin receptor substrate-1 PTB domain, a 7-stranded beta-sandwich, capped by a C-terminal helix. However, the PI domain contains an additional short N-terminal helix and a large insertion between strands 1 and 2, which forms a helix and 2 long connecting loops. The substrate peptide fits into a surface cleft formed from the C-terminal helix and strand 5 [].; GO: 0005515 protein binding; PDB: 1WGU_A 2YT0_A 2YT1_A 2YSZ_A 2ROZ_B 3SO6_A 2DYQ_A 1AQC_A 1X11_B 1WJ1_A ....
Probab=30.48 E-value=1.3e+02 Score=18.30 Aligned_cols=51 Identities=22% Similarity=0.375 Sum_probs=28.8
Q ss_pred ceEEEEEee-cCeEEeeEEeE--EeecceEE--EEehh---hhhhHhhhhHHHHHHHhhhh
Q 040493 9 MQWISYVTQ-SGRLMHVMMTK--IHNVGKVY--HFRAR---RQMAQSIGQVAKFRRRYEQQ 61 (69)
Q Consensus 9 mq~Is~Vtq-~Grl~~vmmt~--~~~~gkvy--h~~aK---rqma~s~GQiAKFKRRf~~~ 61 (69)
++.|||++. +.....++.-. -...+..+ -|... .++.+++||+ |+-.|+..
T Consensus 79 i~~Is~~~~~d~~~~~~Fafi~~~~~~~~~~CHVF~~~~~A~~i~~~i~~a--F~~a~~~~ 137 (140)
T PF00640_consen 79 IRRISFCAVGDPDDKRVFAFIARDPRSSRFYCHVFKCEDQAQEICQAIGQA--FELAYQEF 137 (140)
T ss_dssp GGGEEEEEESSTTETTEEEEEEEETSSSCEEEEEEEESSCHHHHHHHHHHH--HHHHHHHH
T ss_pred ccceEEEEecCCCcceEEEEEeccCCCCccccEeeeHhhHHHHHHHHHHHH--HHHHHHHH
Confidence 578999999 65544443332 22223222 44444 4666778875 77777654
No 27
>PF11102 Cap_synth_GfcB: Group 4 capsule polysaccharide formation lipoprotein gfcB; InterPro: IPR021308 Some members in this bacterial family of proteins are annotated as YjbF however the function is unknown. ; PDB: 2IN5_B.
Probab=26.16 E-value=74 Score=22.05 Aligned_cols=20 Identities=40% Similarity=0.742 Sum_probs=13.7
Q ss_pred CccccceEEE-----EEeecCeEEe
Q 040493 4 GLHPQMQWIS-----YVTQSGRLMH 23 (69)
Q Consensus 4 GlHPqmq~Is-----~Vtq~Grl~~ 23 (69)
|.++|..|+| +|+.+||+..
T Consensus 61 ~~~~~~~W~S~D~~~lvt~~Grlv~ 85 (200)
T PF11102_consen 61 PDTGQLKWLSADGAMLVTRNGRLVK 85 (200)
T ss_dssp ---TEEEEEETTTEEEEEETTEEEE
T ss_pred cccceeEEEcCCCeEEEEeCCEEEE
Confidence 3346788875 8999999863
No 28
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=24.54 E-value=58 Score=21.79 Aligned_cols=15 Identities=53% Similarity=1.066 Sum_probs=11.7
Q ss_pred cceE-EEEEeecCeEE
Q 040493 8 QMQW-ISYVTQSGRLM 22 (69)
Q Consensus 8 qmq~-Is~Vtq~Grl~ 22 (69)
|=|| |+||+++|...
T Consensus 37 LGQWAIGyV~~dg~I~ 52 (86)
T PF02762_consen 37 LGQWAIGYVTQDGKIL 52 (86)
T ss_dssp TTSEEEEEEETTSEEE
T ss_pred ccceeEEEEcCCCcEE
Confidence 3466 99999999753
No 29
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=24.44 E-value=1.8e+02 Score=20.32 Aligned_cols=43 Identities=16% Similarity=0.393 Sum_probs=23.6
Q ss_pred CCCccccceEE---EEEeecCeEEeeEEeEEeecceEE-----EEehhhhhhHhhhhH
Q 040493 2 KKGLHPQMQWI---SYVTQSGRLMHVMMTKIHNVGKVY-----HFRARRQMAQSIGQV 51 (69)
Q Consensus 2 kKGlHPqmq~I---s~Vtq~Grl~~vmmt~~~~~gkvy-----h~~aKrqma~s~GQi 51 (69)
+.|.||++... ++|..+ +.++ ...+.+. ...||...-.++|++
T Consensus 3 ~~~~hpll~~~~~~~~v~~~-----~~~~--~~~~~~~~l~G~n~~GKstll~~i~~~ 53 (222)
T cd03285 3 KEARHPCVEAQDDVAFIPND-----VTLT--RGKSRFLIITGPNMGGKSTYIRQIGVI 53 (222)
T ss_pred cccCCCEEeccCCCCeEEee-----EEEe--ecCCeEEEEECCCCCChHHHHHHHHHH
Confidence 67999999872 122221 1111 1234555 345677766777765
No 30
>PF03221 HTH_Tnp_Tc5: Tc5 transposase DNA-binding domain; InterPro: IPR006600 This entry represents a DNA-binding helix-turn-helix domain found in the pogo family of transposable elements, the centromere protein Cenp-B, and yeast PCD2. There is extensive sequence similarity between Cenp-B and transposase proteins encoded by the pogo superfamily of transposable elements, which includes the human Tigger and Jerky elements []. The HTH domain is composed of three alpha-helices, with the second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, as in other HTHs []. This conserved DNA-binding domain is found in the following proteins: Cenp-B (major centromere autoantigen B or centromere protein B), which appears to organise arrays of centromere satellite DNA into a higher order structure that then direct centromere formation and kinetochore assembly in mammalian chromosomes. The N terminus of Cenp-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA: a psq-type HTH domain followed by a CenpB-type HTH domain, which together bind specifically to the Cenp-B box, which occurs in alpha-satellite DNA in human centromeres []. Pogo family transposable elements includes both Tigger and Jerky elements []. Pogo contains two open reading frames flanked by inverted repeats. The N-terminal region of pogo transposase contains a Cenp-B-type HTH DNA-binding domain []. Mammalian jerky protein, involved in epileptic seizures in mice []. PDC2 (Pyruvate DeCarboxylase 2), which is a transcription factor required for the synthesis of the glycolytic enzyme pyruvate decarboxylase, required for high level expression of both the THI and the PDC genes. PDC2 may be important for a high basal level of PDC gene expression or play a positive role in the autoregulation control of PDC1 and PDC5 [, ]. ; PDB: 1HLV_A 1IUF_A.
Probab=23.69 E-value=45 Score=18.10 Aligned_cols=18 Identities=22% Similarity=0.429 Sum_probs=11.7
Q ss_pred hhhHhhhhHHHHHHHhhh
Q 040493 43 QMAQSIGQVAKFRRRYEQ 60 (69)
Q Consensus 43 qma~s~GQiAKFKRRf~~ 60 (69)
....|.|=+.+|++|++.
T Consensus 45 ~~~~s~~W~~~F~~Rh~i 62 (66)
T PF03221_consen 45 EFKASKGWLDRFKKRHGI 62 (66)
T ss_dssp T-S--CHHHHHHHHHTS-
T ss_pred cCCcccHHHHHHHHHcCC
Confidence 345677889999999954
No 31
>PHA02616 VP2/VP3; Provisional
Probab=22.88 E-value=42 Score=26.07 Aligned_cols=23 Identities=35% Similarity=0.631 Sum_probs=20.0
Q ss_pred CCCccccceEEEEEeecCeEEee
Q 040493 2 KKGLHPQMQWISYVTQSGRLMHV 24 (69)
Q Consensus 2 kKGlHPqmq~Is~Vtq~Grl~~v 24 (69)
+-|.|-+=||||+-+..|.|-|.
T Consensus 160 s~GvHrlGqWiSf~g~tGgTphY 182 (259)
T PHA02616 160 SGGVHRLGQWISFSGETGGTPHY 182 (259)
T ss_pred ccccccccceEEecCCCCCCCCc
Confidence 46999999999999999988653
No 32
>TIGR03667 Rv3369 PPOX class probable F420-dependent enzyme, Rv3369 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN.
Probab=22.11 E-value=2.2e+02 Score=18.08 Aligned_cols=35 Identities=14% Similarity=0.268 Sum_probs=26.8
Q ss_pred cceEEEEEeecCeEEeeEEeEEeecceEEEEehhh
Q 040493 8 QMQWISYVTQSGRLMHVMMTKIHNVGKVYHFRARR 42 (69)
Q Consensus 8 qmq~Is~Vtq~Grl~~vmmt~~~~~gkvyh~~aKr 42 (69)
..-|++.|..+|...-++|.-....|.+|-++...
T Consensus 15 ~~~~LaT~~~dG~P~~~P~~~~~~d~~l~~~t~~~ 49 (130)
T TIGR03667 15 SIVWLTTVRRSGQPQPVPVWFLWDGTEFLIYSRPQ 49 (130)
T ss_pred CeEEEEEECCCCceEEEEEEEEEECCEEEEEeCCc
Confidence 44578888889988888887766788888776654
No 33
>PF11673 DUF3269: Protein of unknown function (DUF3269); InterPro: IPR021687 This entry is represented by Bacteriophage 92, Orf70. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.02 E-value=68 Score=20.78 Aligned_cols=19 Identities=16% Similarity=0.268 Sum_probs=16.1
Q ss_pred hhHHHHHHHhhhhhhhhhc
Q 040493 49 GQVAKFRRRYEQQADAENN 67 (69)
Q Consensus 49 GQiAKFKRRf~~~~~ae~~ 67 (69)
-.+.+||+.|+.+.+.|+.
T Consensus 47 ~El~~fK~~~~L~~~eELg 65 (73)
T PF11673_consen 47 DELKKFKAKHNLLYEEELG 65 (73)
T ss_pred HHHHHHHHHHhhhhHHHhc
Confidence 3689999999999987764
No 34
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=21.29 E-value=48 Score=26.67 Aligned_cols=16 Identities=31% Similarity=0.578 Sum_probs=12.2
Q ss_pred hhhhhhHhhhhHHHHH
Q 040493 40 ARRQMAQSIGQVAKFR 55 (69)
Q Consensus 40 aKrqma~s~GQiAKFK 55 (69)
|---+..-.|||||+|
T Consensus 159 AaGaVGsvvgQiAKlk 174 (340)
T COG2130 159 AAGAVGSVVGQIAKLK 174 (340)
T ss_pred cccccchHHHHHHHhh
Confidence 3445677889999997
No 35
>PF10365 DUF2436: Domain of unknown function (DUF2436); InterPro: IPR018832 Gingipains R and K are endopeptidases with specificity for arginyl and lysyl bonds, respectively. Like other cysteine peptidases, they require reducing conditions for activity. They are maximally active at approximately neutral pH. Gingipains R and K are secreted by the bacterium Porphyromonas gingivalis (Bacteroides gingivalis). The bacterium is a major pathogen in periodontal disease, and the many ways in which the activities of the gingipains may contribute to the disease processes have been reviewed []. These enzymes are also involved in the hemagglutinating activity of the organisms. This entry represents a central region found in gingipain K peptidases, active on lysyl bonds; they belong to the MEROPS peptidase family C25 (gingipain family, clan CD).
Probab=20.23 E-value=1e+02 Score=22.59 Aligned_cols=37 Identities=24% Similarity=0.240 Sum_probs=24.2
Q ss_pred ccc-eEEEEEeecCeEEeeEEeEEeecceEEEEehhhh
Q 040493 7 PQM-QWISYVTQSGRLMHVMMTKIHNVGKVYHFRARRQ 43 (69)
Q Consensus 7 Pqm-q~Is~Vtq~Grl~~vmmt~~~~~gkvyh~~aKrq 43 (69)
||- .+|=+|++.|-----+---.+-.||.|+|+-+++
T Consensus 116 P~~~~kiwIaGd~g~~~tr~dDy~fEAGKtY~ftm~~~ 153 (161)
T PF10365_consen 116 PQPGGKIWIAGDGGDGPTRGDDYVFEAGKTYRFTMKRV 153 (161)
T ss_pred CCCCCeEEEecCCCCCCccccceEEecCCEEEEEEEec
Confidence 554 5666677665444444555678899999987653
No 36
>KOG4521 consensus Nuclear pore complex, Nup160 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.20 E-value=73 Score=30.11 Aligned_cols=44 Identities=30% Similarity=0.402 Sum_probs=32.2
Q ss_pred CccccceEEEEEeecCe-EEee---------------EEeEEeecceEEEEehhhhhhHh
Q 040493 4 GLHPQMQWISYVTQSGR-LMHV---------------MMTKIHNVGKVYHFRARRQMAQS 47 (69)
Q Consensus 4 GlHPqmq~Is~Vtq~Gr-l~~v---------------mmt~~~~~gkvyh~~aKrqma~s 47 (69)
|+||----|||+|++|. +|-+ -|+..-+-+|++++.-|+.+.++
T Consensus 202 g~~Pn~a~~SylTsdgqslfiv~~~S~g~~s~k~pg~t~~~e~k~sklm~~~l~~~~g~a 261 (1480)
T KOG4521|consen 202 GHHPNRATISYLTSDGQSLFIVTLGSYGESSDKHPGFTMGEEGKLSKLMGGTLKRVSGAA 261 (1480)
T ss_pred ccCCCccchhhccccccceEEEEccCCceEeeccCCceEEEEeccccccchhhhcccchh
Confidence 77998888999999998 4433 23334445899999988888743
Done!